Relative Precision of the Sibship and LD Methods for Estimating Effective Population Size With Genomics-Scale Datasets

Computer simulations were used to compare relative precision of 2 widely used single-sample methods for estimating effective population size (Ne)—the sibship method and the linkage disequilibrium (LD) method. Emphasis is on performance when thousands of gene loci are used, which now can easily be achieved even for nonmodel species. Results show that unless Ne is very small, if at least 500–2000 diallelic loci are used, precision of the LD method is higher than the maximum possible precision for the sibship method, which occurs when all sibling relationships have been correctly identified. Results also show that when precision is high for both methods, their estimates of Ne are highly and positively correlated, which limits additional gains in precision that might be obtained by combining information from the 2 estimators.